Abstract

Changes in bacterial gene expression depend not only on the operation of specific transcription factors but also on the regulation exerted by the global physiological condition of the cell. To characterize the influence of this global regulation constitutive genes appear as the most valid model, that can also help us distinguish the impact of physiology on genome organization. However, only a few genes have been investigated so far. Here, we present a large-scale approach to characterize the regulation of the global program by quantifying chromosomal promoter activities of over 700 constitutive genes in Escherichia coli. We identify four response classes (growth-rate dependencies) of which one follows the hyperbolic pattern previously seen. Within this class, we sort genes with respect to their responsiveness to growth rate and examine the association of responsiveness with gene order. Genes showing a particularly sensitive linear response to growth are located near the origin of replication, even when controlling for the increase in the number of replication forks. We then postulate that global regulation could act as a driving force to shape genomic architecture. Evidence is obtained by examining the relation between position conservation of E. coli genes in 100 bacterial species with the number of replication rounds, maximal growth rate and environmental variability of the species' habitat. The response to the physiological state of the cell results therefore in an additional feature contributing to bacterial genome organization.

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